<tool id="3dtrees_standardization" name="3DTrees: LAS/LAZ Standardization" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.2">
    <description>Standardize LAS/LAZ files or validate collections for consistency</description>
    <macros>
        <token name="@TOOL_VERSION@">1.1.0</token>
        <token name="@VERSION_SUFFIX@">0</token>
    </macros>
    <requirements>
        <container type="docker">ghcr.io/3dtrees-earth/3dtrees-pc-standard:@TOOL_VERSION@</container>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        #if $mode.task == 'single_file':
            cp '$mode.input' input.laz &&
            Rscript /src/run.R
            --dataset-path ./input.laz
            --output-dir ./
            --method single_file
            --min-density '$mode.min_density'
            #if $mode.removeable_attributes:
                --removeable_attributes '$mode.removeable_attributes'
            #end if
        #else:
            mkdir -p ./input_files &&
            #for $f in $mode.input_collection
                cp '$f' ./input_files/'${f.element_identifier}.laz' &&
            #end for
            Rscript /src/run.R
            --dataset-path ./input_files/
            --output-dir ./
            --method collection
        #end if
    ]]></command>

    <inputs>
        <conditional name="mode">
            <param name="task" type="select" label="Mode">
                <option value="single_file">Single File Standardization</option>
                <option value="collection">Collection Validation</option>
            </param>
            <when value="single_file">
                <param name="input" type="data" format="laz" label="Point Cloud File" 
                       help="LAS/LAZ point cloud file to standardize (CRS validation, density check, format normalization)"/>
                <param argument="--min-density" type="integer" min="1" max="10000" value="10" 
                       label="Minimum Point Density" 
                       help="Minimum acceptable point density in points per square meter. Default: 10 pts/m²"/>
                <param argument="--removeable_attributes" type="text" value="" optional="true"
                       label="Attributes to Remove" 
                       help="Space-separated list of attribute names to remove (e.g., 'Intensity UserData'). Leave empty for auto-detection."/>
            </when>
            <when value="collection">
                <param name="input_collection" type="data" format="laz" multiple="true" label="Point Cloud Collection" 
                       help="Multiple LAZ/LAS files to validate for consistency (CRS homogeneity, attribute consistency, overlaps)"/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="pc_standardized" format="laz" label="standardized" from_work_dir="input.laz">
            <filter>mode['task'] == "single_file"</filter>
        </data>
        <data name="metadata_json" format="json" label="metadata" from_work_dir="input.json">
            <filter>mode['task'] == "single_file"</filter>
        </data>
        <data name="convex_hull" format="geojson" label="convex_hull" from_work_dir="input_convex_hull_wgs84.GeoJSON">
            <filter>mode['task'] == "single_file"</filter>
        </data>
        <data name="collection_summary" format="json" label="collection_summary" from_work_dir="collection_summary.json">
            <filter>mode['task'] == "collection"</filter>
        </data>
    </outputs>
    <tests>
            <test expect_num_outputs="3">
            <conditional name="mode">
                <param name="task" value="single_file"/>
                <param name="input" value="mikro.laz" ftype="laz"/>
                <param name="min_density" value="10"/>
            </conditional>
            <output name="pc_standardized" ftype="laz">
                <assert_contents>
                    <has_size min="1000"/>
                </assert_contents>
            </output>
            <output name="convex_hull" ftype="geojson">
                <assert_contents>
                    <has_json_property_with_text property="type" text="FeatureCollection"/>
                </assert_contents>
            </output>
            <output name="metadata_json" ftype="json">
                <assert_contents>
                    <has_text text='"point_count":[12917]'/>
                    <has_text text='"standardized":[true]'/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <conditional name="mode">
                <param name="task" value="collection"/>
                <param name="input_collection" value="mikro.laz,mikro2.laz" ftype="laz"/>
            </conditional>
            <output name="collection_summary" ftype="json">
                <assert_contents>
                    <has_json_property_with_value property="n_tiles" value="2"/>
                    <has_json_property_with_value property="homogeneous_crs" value="true"/>
                    <has_json_property_with_value property="homogeneous_attribute_names" value="true"/>
                </assert_contents>
            </output>
        </test>
    </tests>

    <help><![CDATA[
**What it does**

This tool supports two modes:

**Single File Mode** (standardization):
Standardizes a single LAS/LAZ file:

1. **LAS Validation**: Runs ``las_check()`` and fixes header issues
2. **Bounding Box**: Validates and corrects header bounding box
3. **Point Density**: Checks density meets minimum threshold
4. **CRS Validation**: Verifies CRS is defined and transformable to EPSG:4978
5. **Land Check**: Confirms centroid is on land (using Natural Earth data)
6. **Format Normalization**: Downgrades Point Data Format to ≤7 for compatibility
7. **Attribute Cleanup**: Optionally removes specified attributes

**Outputs (single file mode):**
- Standardized ``.laz`` file
- Metadata JSON with pre/post standardization info
- Convex hull GeoJSON in WGS84

**Collection Mode** (validation):
Validates consistency of multiple LAS/LAZ files:

- **CRS Homogeneity**: Checks if all files share the same coordinate reference system
- **Attribute Consistency**: Verifies attribute names and types across files
- **Tile Geometry**: Detects overlaps and gaps between tiles
- **Global Statistics**: Computes aggregated statistics across all files
- **Removeable Attributes**: Identifies attributes that are all-NA or constant-zero

**Outputs (collection mode):**
- ``collection_summary.json`` containing collection-level checks and flags, per-file metadata (CRS, attributes, point counts, convex hulls), and suggested removeable attributes for standardization

**Workflow Usage**

For collection-based workflows:
1. Run this tool with **Collection Validation** first to check consistency
2. Use the suggested ``removeable_attributes`` from the collection summary
3. Then run this tool with **Single File Standardization** (Galaxy maps over collection automatically) for standardization

    ]]></help>

    <creator>
        <person name="Julian Frey" email="julian.frey@wwd.uni-freiburg.de" url="https://orcid.org/0000-0001-7895-702X"/>
        <person name="Janusch Vajna-Jehle" email="janusch.jehle@geosense.uni-freiburg.de" url="https://orcid.org/0009-0002-0034-9387"/>
        <person name="Kilian Gerberding" email="kilian.gerberding@geosense.uni-freiburg.de" url="https://orcid.org/0009-0002-5001-2571"/>
        <person name="Mirko Mälicke" identifier="0000-0002-0424-2651"/>
        <organization name="3Dtrees-Team, University of Freiburg" url="https://github.com/3dTrees-earth"/>
    </creator>

    <citations>
        <citation type="bibtex">
            @misc{3dtrees_standard, title = {3D Trees Standardization}, author = {3D Trees Project}, year = {2025}}
        </citation>
    </citations>
</tool>